2026-07-27 20:26
ftp://ftp.de.debian.org/debian/pool/main/j/jellyfish1/jellyfish1_1.1.11.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=googletest  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j1
platform: Linux-6.12.90+deb13.1-amd64-x86_64-with-glibc2.41
python: 3.12.13
client-version: 1.4.0
compiler: g++ (Debian 14.2.0-19) 14.2.0
cppcheck: head 2.21.0
head-info: 422e90c (2026-07-27 08:53:51 +0200)
count: 167 166
elapsed-time: 0.6 0.4
head-timing-info:

old-timing-info:

head results:
jellyfish-1.1.11/jellyfish/allocators_mmap.cc:26:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ptr [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/allocators_mmap.cc:45:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_PAGESIZE [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/allocators_mmap.cc:50:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nb_threads [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/allocators_mmap.cc:55:21: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/allocators_mmap.cc:56:21: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/allocators_mmap.cc:66:17: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/cite.cc:53:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/dbg.cc:46:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable zero [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/dbg.cc:59:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable signal_handler [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/dump_fastq_main.cc:36:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/dump_main.cc:69:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable die [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/dump_main.cc:77:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/dump_main.cc:35:28: style: Argument 'args' shadows outer variable [shadowVariable]
jellyfish-1.1.11/jellyfish/dump_main.cc:31:11: note: Shadowed variable
jellyfish-1.1.11/jellyfish/dump_main.cc:35:28: note: Shadow argument
jellyfish-1.1.11/jellyfish/err.cc:26:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/file_parser.cc:31:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/file_parser.cc:48:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FileParserError [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/file_parser.cc:77:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _is_mmapped [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/file_parser.cc:86:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _is_mmapped [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/file_parser.cc:36:11: warning:inconclusive: Either the condition 'fd==-1' is redundant or read() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg]
jellyfish-1.1.11/jellyfish/file_parser.cc:32:9: note: Assuming that condition 'fd==-1' is not redundant
jellyfish-1.1.11/jellyfish/file_parser.cc:36:11: note: Invalid argument
jellyfish-1.1.11/jellyfish/file_parser.cc:51:19: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/generate_sequence.cc:57:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable die [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/generate_sequence.cc:67:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/generate_sequence.cc:84:51: style: Variable 'e' can be declared as reference to const [constVariableReference]
jellyfish-1.1.11/jellyfish/hash_fastq_merge.cc:28:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable quadratic_reprobes [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/hash_merge.cc:116:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable die [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/hash_merge.cc:52:17: warning: Member variable 'writer_buffer::full' has no initializer. [uninitMemberVarNoCtor]
jellyfish-1.1.11/jellyfish/hash_merge.cc:57:25: warning: Member variable 'writer_info::done' has no initializer. [uninitMemberVarNoCtor]
jellyfish-1.1.11/jellyfish/hash_merge.cc:59:25: warning: Member variable 'writer_info::out' has no initializer. [uninitMemberVarNoCtor]
jellyfish-1.1.11/jellyfish/hash_merge.cc:60:25: warning: Member variable 'writer_info::buffers' has no initializer. [uninitMemberVarNoCtor]
jellyfish-1.1.11/jellyfish/hash_merge.cc:64:23: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/histo_fastq_main.cc:64:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/histo_main.cc:98:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/histo_main.cc:78:8: style:inconclusive: Either there is a missing 'override', or the member function 'histogram < raw_inv_hash_query_t >::print' can be const. [functionConst]
jellyfish-1.1.11/jellyfish/histo_main.cc:78:8: style:inconclusive: Either there is a missing 'override', or the member function 'histogram < hash_query_t >::print' can be const. [functionConst]
jellyfish-1.1.11/jellyfish/jellyfish.cc:72:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/jellyfish.cc:112:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/jellyfish.cc:118:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/jellyfish.cc:124:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/jellyfish.cc:145:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/jellyfish.cc:75:17: style: Variable 'ccmd' can be declared as pointer to const [constVariablePointer]
jellyfish-1.1.11/jellyfish/mapped_file.cc:20:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_PAGESIZE [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:49:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:54:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:136:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parser [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:186:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parser [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:235:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parser [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:268:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parser [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:302:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parser [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:327:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable die [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:103:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ignore [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , inv_hash_t >::parser' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , inv_hash_t >::ary' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , inv_hash_t >::hash' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , inv_hash_t >::dumper' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , inv_hash_t >::parser' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , inv_hash_t >::ary' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , inv_hash_t >::hash' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , inv_hash_t >::dumper' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , direct_index_t >::parser' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , direct_index_t >::ary' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , direct_index_t >::hash' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_dna , direct_index_t >::dumper' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , direct_index_t >::parser' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , direct_index_t >::ary' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , direct_index_t >::hash' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_qual_dna , direct_index_t >::dumper' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_quake , fastq_hash_t >::parser' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_quake , fastq_hash_t >::ary' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_quake , fastq_hash_t >::hash' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:82:12: warning: Member variable 'mer_counting < jellyfish :: parse_quake , fastq_hash_t >::dumper' is not initialized in the constructor. [uninitMemberVar]
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: style: The destructor '~mer_counting < jellyfish :: parse_dna , inv_hash_t >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:63:12: note: Virtual destructor in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: note: Destructor in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:121:8: style: The function 'count' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:64:16: note: Virtual function in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:121:8: note: Function in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:125:16: style: The function 'get_writing_time' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:65:16: note: Virtual function in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:125:16: note: Function in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:126:20: style: The function 'get_distinct' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:66:20: note: Virtual function in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:126:20: note: Function in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:127:20: style: The function 'get_total' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:67:20: note: Virtual function in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:127:20: note: Function in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: style: The destructor '~mer_counting < jellyfish :: parse_qual_dna , inv_hash_t >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:63:12: note: Virtual destructor in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: note: Destructor in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: style: The destructor '~mer_counting < jellyfish :: parse_dna , direct_index_t >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:63:12: note: Virtual destructor in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: note: Destructor in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: style: The destructor '~mer_counting < jellyfish :: parse_qual_dna , direct_index_t >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:63:12: note: Virtual destructor in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: note: Destructor in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: style: The destructor '~mer_counting < jellyfish :: parse_quake , fastq_hash_t >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
jellyfish-1.1.11/jellyfish/mer_counter.cc:63:12: note: Virtual destructor in base class
jellyfish-1.1.11/jellyfish/mer_counter.cc:86:4: note: Destructor in derived class
jellyfish-1.1.11/jellyfish/mer_counter.cc:378:3: error: Memory leak: counter [memleak]
jellyfish-1.1.11/jellyfish/mer_counter.cc:48:32: style: Parameter 'err' can be declared as reference to const. However it seems that 'die_on_error' is a callback function, if 'err' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
jellyfish-1.1.11/jellyfish/mer_counter.cc:107:39: note: You might need to cast the function pointer here
jellyfish-1.1.11/jellyfish/mer_counter.cc:48:32: note: Parameter 'err' can be declared as reference to const
jellyfish-1.1.11/jellyfish/mer_counter.cc:53:33: style: Parameter 'err' can be declared as reference to const. However it seems that 'warn_on_error' is a callback function, if 'err' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
jellyfish-1.1.11/jellyfish/mer_counter.cc:105:39: note: You might need to cast the function pointer here
jellyfish-1.1.11/jellyfish/mer_counter.cc:53:33: note: Parameter 'err' can be declared as reference to const
jellyfish-1.1.11/jellyfish/mersenne.cpp:30:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mt [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mersenne.cpp:56:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MERS_N [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mersenne.cpp:77:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mti [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mersenne.cpp:167:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LastInterval [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/mersenne.cpp:162:13: style: The scope of the variable 'bran' can be reduced. [variableScope]
jellyfish-1.1.11/jellyfish/mersenne.cpp:69:13: style: Local variable 'i' shadows outer variable [shadowVariable]
jellyfish-1.1.11/jellyfish/mersenne.cpp:47:8: note: Shadowed variable
jellyfish-1.1.11/jellyfish/mersenne.cpp:69:13: note: Shadow local variable
jellyfish-1.1.11/jellyfish/misc.cc:56:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/misc.cc:25:19: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/misc.cc:25:13: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
jellyfish-1.1.11/jellyfish/parse_dna.cc:30:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buffer_size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/parse_quake.cc:29:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seam [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/parse_quake.cc:49:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buffer_size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/parse_quake.cc:34:29: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/parse_qual_dna.cc:29:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seam [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/parse_qual_dna.cc:49:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buffer_size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/parse_qual_dna.cc:34:29: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/parse_read.cc:23:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fparser [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/query_main.cc:42:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable die [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/query_main.cc:52:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/query_main.cc:42:32: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/read_parser.cc:30:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FileParserError [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/read_parser.cc:40:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_nb_reads [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/read_parser.cc:66:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_nb_reads [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/seq_qual_parser.cc:31:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FileParserError [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/seq_qual_parser.cc:47:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FastqSeqQualParserError [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/seq_qual_parser.cc:131:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FastqSeqQualParserError [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/seq_qual_parser.cc:92:12: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
jellyfish-1.1.11/jellyfish/seq_qual_parser.cc:109:14: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
jellyfish-1.1.11/jellyfish/sequence_parser.cc:32:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FileParserError [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/sequence_parser.cc:40:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _eof [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/sequence_parser.cc:67:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _eof [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:34:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:52:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:65:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:81:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:122:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:137:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:142:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:151:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MismatchingSize [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:219:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable columns [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:137:13: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:138:13: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:142:12: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:144:12: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/square_binary_matrix.cc:47:49: style: Variable 'e' can be declared as reference to const [constVariableReference]
jellyfish-1.1.11/jellyfish/stats_main.cc:51:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/test_double_fifo_input.cc:72:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable die [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/test_double_fifo_input.cc:41:17: style:inconclusive: Technically the member function 'display_kmer::get_count' can be const. [functionConst]
jellyfish-1.1.11/jellyfish/test_double_fifo_input.cc:63:17: style:inconclusive: Either there is a missing 'override', or the member function 'parser::get_count' can be const. [functionConst]
jellyfish-1.1.11/jellyfish/test_double_fifo_input.cc:30:43: style: Parameter 'oval' can be declared as pointer to const [constParameterPointer]
jellyfish-1.1.11/jellyfish/test_read_parser.cc:44:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/thread_exec.cc:24:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/thread_exec.cc:36:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Error [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/thread_exec.cc:41:30: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/thread_exec.cc:40:40: style:inconclusive: Function 'start_routine' argument 1 names different: declaration '<unnamed>' definition '_info'. [funcArgNamesDifferentUnnamed]
jellyfish-1.1.11/jellyfish/yaggo.cpp:153:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/jellyfish/yaggo.cpp:30:47: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/yaggo.cpp:43:47: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/yaggo.cpp:56:44: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/yaggo.cpp:69:44: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/yaggo.cpp:82:36: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/yaggo.cpp:95:38: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/yaggo.cpp:108:37: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/jellyfish/yaggo.cpp:121:32: style: C-style pointer casting [cstyleCast]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-filepath.cc:109:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _POSIX_PATH_MAX [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-filepath.cc:351:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pathname_ [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-port.cc:469:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTEST_INFO [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-port.cc:478:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-port.cc:658:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GTEST_FLAG_PREFIX_ [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-port.cc:684:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-port.cc:736:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-printers.cc:205:14: debug: Failed to instantiate template "PrintAsCharLiteralTo". The checking continues anyway. [templateInstantiation]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-test-part.cc:52:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kStackTraceMarker [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-test-part.cc:61:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kSuccess [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-test-part.cc:79:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable array_ [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-test-part.cc:98:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable original_reporter_ [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest-test-part.cc:104:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable has_new_fatal_failure_ [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/gtest/src/gtest.cc:3545:12: error: There is an unknown macro here somewhere. Configuration is required. If GTEST_NAME_ is a macro then please configure it. [unknownMacro]
jellyfish-1.1.11/unit_tests/gtest/src/gtest_main.cc:35:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/test_offsets_key_value.cc:36:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key_len [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/test_square_binary_matrix.cc:12:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/test_square_binary_matrix.cc:22:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/test_square_binary_matrix.cc:80:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
jellyfish-1.1.11/unit_tests/test_square_binary_matrix.cc:81:7: style: Exception should be caught by reference. [catchExceptionByValue]
jellyfish-1.1.11/unit_tests/test_square_binary_matrix.cc:11:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
diff:
head jellyfish-1.1.11/jellyfish/file_parser.cc:36:11: warning:inconclusive: Either the condition 'fd==-1' is redundant or read() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg]
     jellyfish-1.1.11/jellyfish/file_parser.cc:32:9: note: Assuming that condition 'fd==-1' is not redundant
     jellyfish-1.1.11/jellyfish/file_parser.cc:36:11: note: Invalid argument


DONE